Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(40)

Published: Sept. 22, 2023

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in tree life has proven to be a challenge, hindering understanding evolution and fossil record. This is particularly true species-rich highly varied Mollusca where dramatic inconsistency paleontological, morphological, molecular evidence led long-standing debate about group’s phylogeny nature dozens enigmatic taxa. A critical step needed overcome this issue supplement available genomic data, which plentiful for well-studied lineages, with genomes from rare but key as Scaphopoda. Here, by presenting chromosome-level both extant scaphopod orders leveraging complete spanning Mollusca, we provide strong support Scaphopoda sister taxon Bivalvia, revitalizing morphology-based Diasoma hypothesis originally proposed 50 years ago. Our clock analysis confidently dates split between Bivalvia at ~520 Ma, prompting reinterpretation controversial laterally compressed Early fossils, including Anabarella , Watsonella, Mellopegma, stem diasomes. Moreover, show that incongruence phylogenetic placement previous phylogenomic studies was due ancient incomplete lineage sorting (ILS) occurred rapid radiation Conchifera. findings highlight need consider ILS potential source error deep reconstruction, especially context unique Explosion.

Language: Английский

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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(1), P. 207 - 222

Published: Jan. 1, 2024

Abstract In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying introgression, however, presents challenge. To address this issue, we focused on simple cases involving 3 species known phylogenetic tree. Using mathematical analyses simulations, evaluated performance popular methods, including HyDe PhyloNet/MPL, full-likelihood method, Bayesian Phylogenetics Phylogeography (BPP), in detecting introgression. Our findings suggest that heuristic approaches relying site-pattern counts gene-tree topologies struggle differentiate between sampled non-sister species, frequently leading incorrect identification donor recipient species. The method BPP uses multilocus sequence alignments directly—hence taking into account both branch lengths, by contrast, is capable phylogenomic datasets. We analyzed real-world dataset 14 Jaltomata (Solanaceae) showcase potential methods accurate inference

Language: Английский

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Integrated analyses reveal extensive cytonuclear discordance and two new members of Rhodiola

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 6, 2025

Abstract Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai–Tibet Plateau (QTP) and the mountainous region southwestern China have long been regarded as hotspots. However, despite considerable efforts, numerous plant may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca . 58 perennial herb species, which used an important traditional medicinal for centuries. Rampant exploitation has put some at risk extinction. also recognized a promising model investigating radiation speciation QTP. phylogenetic relationships among major clades genus are not well resolved, underlying causes cytonuclear discordance briefly mentioned previous studies remain unexplored. Through phylogenomic analyses utilizing data from both nuclear genome plastome 42 we identified six found extensive discordance, was primarily attributed to hybridization introgression occurring or closely related species. In addition, integration morphological, phylogenomic, population genomic, ecological evidence resulted identification description new : R. renii sp. nov., reclassification previously Pseudosedum merged into results highlight significant role evolution probably other rapid‐radiated groups QTP, emphasize need increased discovery efforts such QTP its adjacent areas.

Language: Английский

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Exploring the Distribution of Phylogenetic Networks Generated Under a Birth-Death-Hybridization Process

Bulletin of the Society of Systematic Biologists, Journal Year: 2024, Volume and Issue: 2(3), P. 1 - 22

Published: March 15, 2024

Gene-flow processes such as hybridization and introgression play important roles in shaping diversity across the tree of life. Recent studies extending birth-death models have made it possible to investigate patterns reticulation a macroevolutionary context. These allow for different gene flow events that can either add, maintain, or remove lineages—with itself possibly being dependent on relatedness between species—thus creating complex diversification scenarios. Further, many reticulate phylogenetic inference methods assume specific structures phylogenies belonging certain network classes. However, distributions networks under are poorly characterized, is unknown whether they violate common methodological assumptions. We use simulation techniques explore space birth-death-hybridization process where rate linear dependence genetic distance. Specifically, we measured number lineages through time role along with proportion belong commonly used classes (e.g., tree-child, tree-based, level-1 networks). find growth class membership largely affected by assumptions about flow. In accordance previous studies, lower belonged these based type density events. process, factors form an antagonistic relationship; cause high proportions also lead highest density, consequently lowering overall some observed distance–dependent incomplete sampling increase membership, primarily due having fewer Our results inform if their biological expectations associated evolutionary histories satisfy current methodology aid finding relevant development.

Language: Английский

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Integrated taxonomy using morphology and DNA sequences: recognition of a new species with comments on the geological history of the Liolaemus capillitas clade (Squamata: Iguania)

Systematics and Biodiversity, Journal Year: 2025, Volume and Issue: 23(1)

Published: Feb. 13, 2025

Language: Английский

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Impact of Ghost Introgression on Coalescent-Based Species Tree Inference and Estimation of Divergence Time

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(1), P. 35 - 49

Published: July 7, 2022

Abstract The species studied in any evolutionary investigation generally constitute a small proportion of all the currently existing or that have gone extinct. It is therefore likely introgression, which widespread across tree life, involves “ghosts,” is, unsampled, unknown, extinct lineages. However, impact ghost introgression on estimations trees has rarely been and poorly understood. Here, we use mathematical analysis simulations to examine robustness methods based multispecies coalescent model from extant lineage. We found many results originally obtained for between can easily be extended such as strongly interactive effects incomplete lineage sorting (ILS) occurrence anomalous gene trees. relative performance summary method (ASTRAL) full-likelihood (*BEAST) varies under different scenarios, with former being more robust flow nonsister species, whereas latter performing better certain conditions introgression. When an outgroup (defined diverged before most basal investigation) acts donor introgressed genes, time root divergence among investigated was overestimated, ingroup commonly perceived, only lead underestimation. In cases may not involve lineages, stronger ILS, higher accuracy achieved estimating divergence, although topology prone biased by effect [Anomalous trees; time; introgression; coalescent; simulation; tree.]

Language: Английский

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Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)

Evolution, Journal Year: 2024, Volume and Issue: 78(4), P. 716 - 733

Published: Jan. 23, 2024

Abstract Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, signals exhibited by each dimension may not converge. In such scenarios, incomplete sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci 90 individuals), (linear geometric traits 823 411 individuals, respectively), spatial, climatic data to reconstruct evolutionary history a speciation continuum liolaemid lizards (Liolaemus kingii group). Specifically, (a) inferred population structure group contrasted it with variability; (b) assessed role postdivergence flow shaping phylogeographic patterns; (c) explored ecogeographic drivers diversification across time space. We eight clusters exhibiting leaky genetic borders coincident geographic transitions. also found evidence resulting transgressive evolution one species. Predicted ancestral niches unveiled suitable areas southern eastern Patagonia during glacial interglacial periods. Our study underscores integrating different model-based approaches determine underlying causes diversification, challenge faced recently diverged groups. highlight Liolaemus as model system for broader studies.

Language: Английский

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Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 202, P. 108222 - 108222

Published: Oct. 30, 2024

Language: Английский

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Diversification and Biogeography of North American Thistles (Cirsium: Carduoideae: Compositae): Drivers of a Rapid Continent-Wide Radiation

International Journal of Plant Sciences, Journal Year: 2023, Volume and Issue: 184(5), P. 322 - 341

Published: Jan. 23, 2023

Premise of research. Cirsium ("thistles"), the most speciose genus in Compositae (Asteraceae) subfamily Carduoideae native to North America, comprises a rapid endemic radiation. Hummingbird pollination is rare Compositae, but approximately 10% all America are adapted this syndrome. Although an example continent-wide evolutionary radiation, biotic and abiotic factors contributing remarkable diversification have never been studied.Methodology. Sixty-four taxa representing its distribution were sequenced using MYbaits 1061 1kv1 kit. These results used infer time-calibrated phylogeny estimate divergence times rates. Ancestral area reconstructions for eight biogeographical areas 10 habitats performed with BioGeoBEARS. A model-fitting approach was test whether (1) different environmental variables related diversification, (2) pollinator type differences environment, (3) diversification. Phylogenetic least squares models against rates variables, type, or morphological traits influenced diversification.Pivotal results. originated 2 mya, majority occurring three nearly simultaneous bursts during onset Pleistocene ice age. showed evidence phylogenetic signal, there no significant innovations that contributed overall Cirsium. Precipitation semiaridity main catalysts associated near-significant lower than insect pollination.Conclusions. The integrated effects niche conservatism glacial-interglacial cycles played role shaping current distributional patterns, particularly alpine mountain systems canyons Colorado Plateau. hummingbird Cirsium, switch syndrome may facilitated expansion across post-Pleistocene fragmented landscapes. Ultimately, study offers important insights into drivers rapid, radiation impact glaciation on flora America.

Language: Английский

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Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 188, P. 107912 - 107912

Published: Aug. 29, 2023

Language: Английский

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